Arguments

x

Numerical data frame or matrix (observations x variables), or
ExpressionSet object with non empty assayData and phenoData; NAs are allowed
for PLS-DA but for SVM, samples with NA will be removed

...

Currently not used.

y

Two-level factor corresponding to the class labels, or a character
indicating the name of the column of the pData to be used, when x is an
ExpressionSet object

methodVc

Character vector: Either one or all of the following
classifiers: Partial Least Squares Discriminant Analysis ('plsda'), or
Random Forest ('randomforest'), or Support Vector Machine ('svm')

bootI

Integer: Number of bootstaps for resampling

pvalN

Numeric: To speed up the selection, only variables which
significantly improve the model up to two times this threshold (to take into
account potential fluctuations) are computed

permI

Integer: Random permutation are used to assess the significance
of each new variable included into the model (forward selection)

fixRankL

Logical: Should the initial ranking be computed with the
full model only, or as the median of the ranks from the models built on the
sampled dataset?

printL

Logical: Should informations regarding the data set and the
model be printed? [default = TRUE]

plotL

Logical: Should the 'summary' plot be displayed? [default =
TRUE]

.sinkC

Character: Name of the file for R output diversion [default =
NULL: no diversion]; Diversion of messages is required for the integration
into Galaxy

Value

An S4 object of class 'biosign' containing the following slots: 1)
'methodVc' character vector: selected classifier(s) ('plsda',
'randomforest', and/or 'svm'), 2) 'accuracyMN' numeric matrix: balanced
accuracies for the full models, and the models restricted to the 'S' and
'AS' signatures (predictions are obtained by using the resampling scheme
selected with the 'bootI' and 'crossvalI' arguments), 3) 'tierMC' character
matrix: contains the tier ('S', 'A', 'B', 'C', 'D', or 'E') of each feature
for each classifier (features with tier 'S' have been found significant in
all backward selections; features with tier 'A' have been found significant
in all but the last selection, and so on), 4) modelLs list: selected
classifier(s) trained on the subset restricted to the 'S' features, 5)
signatureLs list: 'S' signatures for each classifier; and 6) 'AS' list: 'AS'
signatures and corresponding trained classifiers, in addition to the dataset
restricted to tiers 'S' and 'A' ('xMN') and the labels ('yFc')